Abstract

Background

Profile Hidden Markov Model (HMM) is a powerful statistical model to represent a family
of DNA, RNA, and protein sequences. Profile HMM has been widely used in bioinformatics
research such as sequence alignment, gene structure prediction, motif identification,
protein structure prediction, and biological database search. However, few comprehensive,
visual editing tools for profile HMM are publicly available.

Results

We develop a visual editor for profile Hidden Markov Models (HMMEditor). HMMEditor
can visualize the profile HMM architecture, transition probabilities, and emission
probabilities. Moreover, it provides functions to edit and save HMM and parameters.
Furthermore, HMMEditor allows users to align a sequence against the profile HMM and
to visualize the corresponding Viterbi path.

Conclusion

HMMEditor provides a set of unique functions to visualize and edit a profile HMM.
It is a useful tool for biological sequence analysis and modeling. Both HMMEditor
software and web service are freely available.